intraBplot: Intra-samples Karlin B plot

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Plot CU frequency distances between two samples (given by x and y).

Usage

intraBplot(x, y, names = c("x", "y"), variable, ribosomal = FALSE,
  size = 1, alpha = 0.5)

## S4 method for signature 'codonTable,codonTable'
intraBplot(x, y, names = c("x", "y"),
  variable, ribosomal = FALSE, size = 1, alpha = 0.5)

Arguments

x, y	Objects of codonTable class.
names	Character vector of length 2, giving names for samples.
variable	A character, name of the function that will be used to calculate CU statistic values for plotting. Must be one of the following: c("MILC", "B", "MCB", "ENCprime").
ribosomal	Logical, whether to indicate ribosomal genes in the plot. Default is FALSE.
size	Numeric, indicating points' size
alpha	Numeric, between 0 and 1, indicating points' transparency (default is 0.1).

Value

A ggplot object.

Examples

require(ggplot2)
# calculate MILC distance to the average CU of the example DNA sequences,
# and to the average CU of ribosomal genes among the example DNA sequences
milc <- MILC(LD94, self = TRUE, ribosomal = TRUE)

intraBplot(x = HD59, y = LD94, names = c("HD59", "LD94"),
           variable = "MILC", size = 3)

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.